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count_linkage() accepts a subject_names argument but doesn't subset on it

bugSomething isn't workingSomething isn't working

Status: Open.

#168 In FertigLab/dominoSignal;

· kjkrishnan opened on Mar 3, 2026

summarize_linkages linkage loops will error when vector is empty

bugSomething isn't workingSomething isn't working

Status: Open.

#167 In FertigLab/dominoSignal;

· kjkrishnan opened on Mar 3, 2026

gene_network() mutates OutgoingSignalingClust by prefixing "L_" inside the loop. If multiple clusters are processed this can lead to incorrect column selection / plot titles.

bugSomething isn't workingSomething isn't working

Status: Open.

#166 In FertigLab/dominoSignal;

· kjkrishnan opened on Mar 3, 2026

create_domino() documents a use_clusters argument, but it is not used anywhere in the function

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#165 In FertigLab/dominoSignal;

· kjkrishnan opened on Mar 3, 2026

Errors for input validation are vague

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#164 In FertigLab/dominoSignal;

· kjkrishnan opened on Mar 3, 2026

Network plots with clusters

enhancementNew feature or requestNew feature or request

Status: Open.

#160 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

Combining replicates

enhancementNew feature or requestNew feature or request

Status: Open.

#159 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

Convert object to data frame

enhancementNew feature or requestNew feature or request

Status: Open.

#158 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

gene_network plot title is not working for more than one cluster in the clust argument with no OutgoingSignalingClust

bugSomething isn't workingSomething isn't working

Status: Open.

#157 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

gene_network plot giving subscript out of bounds error if vectors of clusters are passed to clust and OutgoingSignalingClust. For example:

bugSomething isn't workingSomething isn't working

Status: Open.

#156 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

signaling_network gives an error requiring finite 'xlim' values when using the showIncomingSignalingClusts argument. For example, if I wanted to look at incoming signal to the CD8 T cell clusters:

bugSomething isn't workingSomething isn't working

Status: Open.

#155 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026

circos_ligand_receptor is sometimes throwing an error at the step where expression values are obtained from cl_signaling matrices (ex. LILRB2). However, this is inconsistent. For example,

bugSomething isn't workingSomething isn't working

Status: Open.

#154 In FertigLab/dominoSignal;

· kjkrishnan opened on Feb 24, 2026